David Haussler

Growing International Genomics Movement to Sequence Earth’s Vertebrate Life Has Roots at UC Santa Cruz

Initiative Conceived in 2009 Expands with Goal to Generate Complete Genome Assemblies of All 66,000 Vertebrate Species

SANTA CRUZ, CA – September 12, 2018  – The Genome 10K (G10K) consortium, co-founded nearly a decade ago at UC Santa Cruz by UC Santa Cruz Genomics Institute Scientific Director David Haussler, announced a new initiative — the international Vertebrate Genomes Project (VGP). VGP’s mission is to generate high-quality, near error-free, complete genome assemblies of all 66,000 vertebrate species on Earth. The hope is that this information will be leveraged to address fundamental questions in biology, conservation, and disease.

The G10K originated in April 2009 at a three-day meeting held at the University of California, Santa Cruz. By fall 2009, the project had recruited more than 68 scientists. Calling themselves the Genome 10K Community of Scientists (G10KCOS), the group published a paper that fall proposing to collect the genomes of 10,000 vertebrate species.

Between 2009 and 2015, the G10K organized volunteer stewards, who actually exceeded the original goal by contributing to a specimen catalog of more than 16,000 vertebrate species. These included living and recently extinct mammals, birds, non-avian reptiles, amphibians, and fishes — many of which are threatened or endangered. Community stewards represented institutions playing major roles in sample disposition and were responsible for making certain that samples are documented and preserved.

During this period, the G10k also conducted two “Assemblathons” and one “Alignathon.” Assemblathons were collaborative efforts designed to spur improvements in computational methods for genome assembly. Participating teams used their own software to assemble one or more genomes that the organizers provide. The Alignathon, led by UCSC Professor Benedict Paten, assessed whole genome aligners and promoted development of the field of whole genome alignment.

Meanwhile, technologies and platforms for sequencing, assembling and aligning genomes were advancing at a rapid pace, similar to the last decade’s advances in digital photography. These advances enabled “high-resolution” haplotyped reference genomes to replace low-resolution, lower-value reference genomes assembled during initial phases of the project. Between 2015 and 2018, the G10K-VGP turned its focus to advancing and developing technologies necessary to create these high-quality, platinum-level reference genomes assemblies.

The G10K consortium now counts more than 150 experts from academia, industry, and government, from over 50 institutions and 12 countries — including experts from the UC Santa Cruz Genomics Institute.

In 2018, the G10K consortium group was a key force in the creation of the largest genome sequencing project to date, the Earth BioGenome Project (EBP). The ultimate goal of the EBP is to sequence the DNA of each known complex life form on Earth, including all known plants, animals and fungi. To date, the genomes of fewer than 0.2 percent of such species have been sequenced.

In a paper published April 23, 2018 in the Proceedings of the National Academy of Sciences (PNAS), the international team behind the Earth BioGenome Project pointed to the extremely successful Human Genome Project as a reason why this type of research needs funding.

Launched in 1990 and completed in 2003, the Human Genome Project was another international collaboration that invested approximately $3 billion towards sequencing the entire human genome. The resulting “genomic revolution” has had an enormous impact not only on human medicine but also on veterinary medicine, agricultural bioscience, biotechnology, environmental science, renewable energy, forensics and industrial biotechnology. A 2013 report by the Battelle Memorial Institute estimated the financial benefit of the Human Genome Project to the U.S. economy alone to be nearly $1 trillion.

Dr. Haussler headed the UC Santa Cruz team of the Human Genome Project had the honor of posting the first draft of the human genome on the Internet in 2000.

“The success of the Human Genome Project continues to inspire ever-more ambitious genomics initiatives,” Haussler said. “It would be irresponsible not to undertake projects to sequence other species given our extraordinary new capacity to sequence DNA,” he continued. “Humans are the stewards of life on Earth. To be responsible stewards of life, we must start by understanding it.”

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About the UC Santa Cruz Genomics Institute

Comprised of diverse researchers from a variety of disciplines across three academic divisions, the UC Santa Cruz Genomics Institute leads UC Santa Cruz’s efforts to unlock the world’s genomic data and accelerate breakthroughs in health and evolutionary biology. Our platforms, technologies, and scientists unite global communities to create and deploy data-driven, life-saving treatments and innovative environmental and conservation efforts.

About the Baskin School of Engineering

Home to the UC Santa Cruz Genomics Institute, the Baskin School of Engineering at UC Santa Cruz offers unique opportunities for education, research and training. Faculty and students seek new approaches to critical 21st century challenges within the domains of data science, genomics, bioinformatics, biotechnology, statistical modeling, high performance computing, sustainability engineering, human-centered design, communications, cyberphysical systems, optoelectronics and photonics, and networking. By leveraging novel tools that emerge from changing technologies, we have pioneered new engineering approaches and disciplines, examples of which include biomolecular engineering, computational media, and technology and information management.